Abstract: Hydroponics has become the optimal method for plant nutrition research. The technology can control rhizosphere nutrition via a change in nutrient solution. However, hydroponic culture technology in Arabidopsis thaliana can not be widely used because of root ventilation and microbe creation. In this work, we combined medium germination with hydroponic culture by using Eppendorf tubes and a centrifuge tube box. The problem of root ventilation was resolved by controlling the nutrition culture, reducing culture depth and increasing the surface area. The rapid equilibrium of agar and nutrient solution was achieved by using a centrifugal tube cover as supporting material, which could reduce the evaporation of water and the dosage and thickness of agar. We provide a simple and economical hydroponic method for culture of A. thaliana and nutrition stress research.